On 2011-12-12 09:54, sulatha M. S wrote:
Dear David,
Yes it is DGact.
The DGeq follows from the fraction of COOH that are not forming
hydrogen bonds, option -nhbdist.
So, I need to use the equation (9) and (10) from your paper to calculate
the equilibrium constant and free energy of H-bonding.
Yes.
Another question I have is, for a polycarboxylic acid system in
water
(COOH groups as side chains) for a 10ns run, I got the following
as the
output where the life time of the H-bond (between the polyacid and
water) is negative. Is this correct?
This means that the ACF has not equilibrated and you need much
longer sims. You probably got a warning about it.
I did not get a warning here. I also have simulations (20ns) of
copolyacids where again it gave me negative life time. These runs are
well equilibrated with respect to energy and Rg of the polymers. The
system is a 20 repeat unit chain in approx. 5500 water molecules. I have
done simulations in which 10 units are COO- and the remaining 10 as COOH
along the chain. With a 10ns trajectory, the average life time of
H-bonds is positive.Only in the case of unionized acid I am getting a
negative life time.
Did you look at the ACF graph? It could be constant at 1 or 0.
ACF 22057/22057
Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 0.0146697
Q = 0
--------------------------------------------------
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward -0.271 -3.687 -666.000 0.0146697
Backward -2.291 -0.437 -666.000
One-way 0.101 9.882 10.207
Integral 0.034 29.376 12.907
Relaxation 0.063 15.803 11.370
Thankyou for any help,
Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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What is the value for free energy of H-bonding.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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